[gmx-users] position restraints

[Shima Arasteh]

Dear gmx users,

I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. 
After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. 
Is there any step which I have not done to set the restraints correctly?


Thanks in advance.

Sincerely,
Shima